MS in Bioinformatics or MS in Computer Science with a concetration in Bioinformatics?

[Kimist99]

Hello!

I'm currently in a Biomedical Informatics department but I'm finding my knowledge base is significantly lacking compared to what my interests are ie natural language processing, biological ontologies, statistical genomics ect.

My advisor has suggested I take about 6 or so courses in CS in additon to those required for my degree Biomedical Informatics. However, I'm thinking if I take those courses I may as well switch departments especialy considering that CS majors appear to have a significant advantage competing for gigs in Bioinformatics.

FYI, my background is in Molecular Biology/Biochemisty/cancer research and I've also learned a few programming languages including Perl, Python, and R. My long term goal is to complete the PhD.

Anyone have any thoughts?

[blancha]

Pros of choosing computer science:
- Computer scientists are rich. Bioinformaticians are poor. :'-(
- It is easier for a computer scientist to work in bioinformatics, than for a bioinformatician to work in a field of computer science other than bioinformatics.

Cons of choosing computer science:
- You are missing a lot of the theoretical foundations of computer science. This is highly dependent on the department, but you may struggle in your graduate studies if you don't have solid foundations in mathematics and algorithmics. Also, all the language you have learned are higher level languages. You don't mention C/C++ or even Java.
- People in bioinformatics come from more diverse backgrounds and have more varied interests. You tend to find more asocial students in computer science, who spend most of their time interacting with a computer.

In the end, it's really up to your personal interests. You must remember that in graduate studies, you will be doing original research. You have to be quite passionate about your field of study. It's not like undergraduate studies where you just follow the course given by the professor.

Incidentally, I have no phD but multiple degrees in computer science, molecular biology and bioinformatics.
I am quite jealous of my old classmates in computer science who make far more money than I do. On the other hand, I enjoy interacting with wet lab biologists, and find rather dull people who spend all day interacting with a machine.

[Brian Bushnell]

Pros of choosing computer science:
- It is easier for a computer scientist to work in bioinformatics, than for a bioinformatician to work in a field of computer science other than bioinformatics.

I agree with this. I think going into pure bioinformatics is specializing too early, and would be detrimental to you career-wise if you want flexibility.

[Kimist99]

Thanks for the responses!

Blanca, I have an MS degree in Chemistry and have spent 10+ years on the research bench. However, without a doctorate, it's pretty much a dead end career. The first programming course I took was Java but so far, I haven't seen it's utility in Biomedical Informatics, excluding Natural Language Processing. I didn't mention it because I haven't needed to use it so far and it isn't the "go to" language in Bioinformatics. Diffeq was required for my BS in Chemistry but I haven't had any math beyond that.

Brian, I think the field of Biomedical Informatics is quite flexible and there are a number of area's one can target. I'm specifically targeting Translational Informatics and most of the people I've met in this area were computer scientists at some point in their careers. That said, I'm not interested in strictly being a computer scientist in part because I prefer more "social" collegues.

Thanks again!

[Brian Bushnell]

There's a lot of Java code in bioinformatics, particularly from the Broad Institute. You can write bioinformatic code in any language... but it's generally written in Perl, Python, R, C/C++, or Java. Of those, the first three tend to be slower.

If you don't want to ever do pure CS, that's a good reason to look at bioinformatics. So, I would say the choice also comes down to the question of whether you want to primarily develop/install/test/maintain software for bioinformatics, or primarily run software for bioinformatics (i.e., actually do real bioinformatics). If you prefer the latter then probably a pure bioinformatics degree would be better.

Still, a pure CS degree can be much more readily applied to some other applied CS area (say, computational chemistry) if, hypothetically, something changes.

[Kimist99]

There's a lot of Java code in bioinformatics, particularly from the Broad Institute.

I learned GWAS/Statistical Genetics from a course at the Broad Institute, but never needed to code in Java. However, I get your point.

Still, a pure CS degree can be much more readily applied to some other applied CS area (say, computational chemistry) if, hypothetically, something changes.

This is a good point that helps me make my decision to study CS. As I mentioned before, I can concentrate in Bioinformatics even though it will take ~ a year longer to complete because I need so many preq courses. But given the tightness of the job market, I think it will be a year very well spent.

Thanks again!